Theoretical study of conformational disorder and selective adsorption of small organic molecules in the flexible metal-organic framework material MIL-53-Fe

Many of the potential applications for metal-organic framework (MOF) materials require molecular level understanding of their adsorption of small organic molecules, which are not readily accessible from experiment. Through high-level van der Waals corrected, hybrid density functional theory calculations, we elucidate the adsorption configurations of several, representative small organic guest molecules in an archetypal flexible MOF material, MIL-53-Fe. The predicted relative energies between low-energy adsorption configurations of 1,4-benzoquinone in MIL-53-Fe are in very good agreement with the thermal transition temperatures observed experimentally and suggest that thermodynamic factors govern the precise arrangements and loading of guests in the MOF host. Experimentally observed conformational disorder of small organic molecules in MIL-53-Fe is explained by predicted multiple low-energy adsorption configurations that are comparable with the thermal energy of the guests, kT. Finally, we show that the previously observed selective adsorption of pyridine and 2,6-lutidine molecules in water by MIL-53-Fe, can be rationalised through a careful analysis of the host–guest and guest–guest interactions and is controlled by thermodynamic factors.     

Computational screening of ZIFs for CO2 separations

Using molecular simulations, we studied a diverse collection of zeolite–imidazolate frameworks (ZIFs) to evaluate their performances in adsorption- and membrane-based gas separations. Molecular simulations were performed for both single-component gases (CH₄, CO₂, H₂ and N₂) and binary gas mixtures (CO₂/CH₄, CO₂/N₂, CO₂/H₂ and CH₄/H₂) to predict the intrinsic and mixture selectivities of ZIFs. These two selectivities were compared to discuss the importance of multi-component mixture effects on making predictions about the separation performance of a material. Gas separation performances of ZIFs were compared with other nanoporous materials and our results showed that several ZIFs can outperform well-known zeolites and metal–organic frameworks in CO₂ separations. Several other properties of ZIFs such as gas permeability, working capacity and sorbent selection parameter were computed to identify the most promising materials in adsorption- and membrane-based separation of CO₂/CH₄, CO₂/N₂, CO₂/H₂ and CH₄/H₂.     

Antibody informatics for drug discovery

More and more antibody therapeutics are being approved every year, mainly due to their high efficacy and antigen selectivity. However, it is still difficult to identify the antigen, and thereby the function, of an antibody if no other information is available. There are obstacles inherent to the antibody science in every project in antibody drug discovery. Recent experimental technologies allow for the rapid generation of large-scale data on antibody sequences, affinity, potency, structures, and biological functions; this should accelerate drug discovery research. Therefore, a robust bioinformatic infrastructure for these large data sets has become necessary. In this article, we first identify and discuss the typical obstacles faced during the antibody drug discovery process. We then summarize the current status of three sub-fields of antibody informatics as follows: (i) recent progress in technologies for antibody rational design using computational approaches to affinity and stability improvement, as well as ab-initio and homology-based antibody modeling; (ii) resources for antibody sequences, structures, and immune epitopes and open drug discovery resources for development of antibody drugs; and (iii) antibody numbering and IMGT. Here, we review “antibody informatics,” which may integrate the above three fields so that bridging the gaps between industrial needs and academic solutions can be accelerated. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.     

Cartography of littoral rocky-shore communities (CARLIT) as a tool for ecological quality assessment of coastal waters in the Eastern Adriatic Sea

Littoral cartography is a valuable tool which uses shallow water macroalgal communities for monitoring ecosystem health and water quality. Cartography of littoral rocky-shore communities (CARLIT) is a European Union Water Framework Directive-compliant monitoring method widely used in the Western Mediterranean Sea. This non-destructive method is based on a visual observation of the type and length of coast occupied by rocky-shore communities in the upper-sublittoral zone. Here we present the first wide-scale application of CARLIT in the Adriatic Sea. The reference values calculated specifically for the Croatian coast (Eastern Adriatic Sea) ensure accurate calculation of the ecological status. The measured ecological quality ratio values (EQR) show a good linear relation with the Land Uses Simplified Index (LUSI) and appropriately reflect an increase in nutrient concentrations. The results suggest that this method can be used as a reliable biomonitoring tool in the Eastern Adriatic Sea. This study highlighted that Cystoseira forests thrive in 39% of the surveyed coastline and 23% of the coastline seems to be subjected to overgrazing by sea urchins. Our results provide a spatially accurate information on the abundance of different upper-sublittoral communities and the associated ecological status, which can be used in future management plans for improving water quality.     

Non‐continuous reproductive phenology of animal‐dispersed species in young forest restoration plantings

Tree species that produce resources for fauna are recommended for forest restoration plantings to attract pollinators and seed dispersers; however, information regarding the flowering and fruiting of these species during early growth stages is scarce. We evaluated the reproductive phenology of animal‐dispersed tree species widely used in Atlantic Forest restoration. We marked 16 animal‐dispersed tree species in 3‐ to 8‐year‐old forest restoration plantings in Itu‐São Paulo, southeast Brazil. We noted the age of the first reproductive event, flowering and fruiting seasonality, percentage of trees that reached reproductive stages, and intensity of bud, flower, and fruit production for each species. Flowering and fruiting are seasonal for most species; only two, Cecropia pachystachya and Ficus guaranitica, exhibited continuous flowering and fruiting throughout the year; we also identified Schinus terebinthifolia and Dendropanax cuneatus fruiting in the dry season during resource scarcity. Therefore, we recommend all as framework species, that is, species that are animal‐dispersed with early flowering and fruiting potential, for forest restoration. Further, we recommend identifying and planting similar animal‐dispersed tree species that produce fruits constantly or in the dry season to maximize fauna resource availability throughout the year in tropical forest restoration plantings. Abstract in Portuguese is available with online material     

具有自噬抑制作用的卟啉金属有机框架的制备及其光动力癌症治疗的研究*

光动力疗法(PDT)具有微创、可控、低毒、可重复治疗等优点,已成为临床医学中不可缺少的治疗手段。但由于肿瘤细胞的自我保护机制,大大降低了PDT疗效。使用PDT治疗方法的同时实施药理自噬抑制策略,切断因光动力治疗下严重氧化损伤下的保护性自噬。通过油浴加热法合成卟啉金属有机框架PCN-224,并在PCN-224上负载自噬抑制剂硫酸羟氯喹(HCQ),通过扫描电子显微镜(SEM)、粒径测试(DLS)、紫外可见光谱测试等方法检测,结果表明成功地合成了该材料,增强了卟啉光敏剂的水溶性,并且光照后对4T1小鼠乳腺癌细胞毒性明显增强,且装载了HCQ后进一步提高了肿瘤杀伤能力。     

Counterpolitics of Liberation in Contemporary China: Corruption,Law, and Popular Religion

This article explores the hidden transfers between law and religion by focussing on the conditions of existence of ‘liberated’ peasant subjects in contemporary China. The post-Maoist era sought to create new citizens from the collectivised Maoist masses who are subject to market reforms and a new politics of ‘governing through law’ (fazhi). At the same time, new religiousities have blossomed in the Chinese countryside. Representing ‘feudal superstition’, their collective practices remain illegal until today. I argue that, beyond the issue of belief, contemporary ‘feudal superstition’ does not represent a form of anti-secular resistance, but rather confirms the central tenets of Chinese secularism from the perspective of ‘failed’ peasant subjects. Where the realities of market liberalisation and governing through law are experienced as corruption, feudal superstition recreates the conditions to realise liberated peasant subjects: a participatory local public sphere, political visibility, investments in the public good, and a new collective property.     

The Global Sequence Signature algorithm unveils a structural network surrounding heavy chain CDR3 loop in Camelidae variable domains

Background

A large fraction of camelid (camels and llamas) antibodies is composed of heavy chain-only homodimers, able to recognise antigens with their variable domain. Events in somatic assembly and maturation of antibodies such as hypermutations and rearrangement of variable loops (CDRs — complementary determining regions) and selection among a wide range of framework variants are generally considered to be random processes.

Methods

An original algorithmic approach (Global Sequence Signature—GSS) was developed, able to take into account multiple functional and/or local sequence properties to detect scattered evolutionary constraints into sequences.

Results

Using the GSS approach, we show that the length of the main hypervariable loop (CDR3) is linked to the nature of 19 surrounding residues on the scaffold. Surprisingly, the relation between CDR3 size and scaffold residues strongly depends on the considered species, illustrating either significant differences in selection mechanisms or functional constraints during antibody maturation.

Conclusions

Combined with the statistical coupling analysis (SCA) approach at the level of scaffold residues, this study has unravelled a robust interaction network on antibody structure surrounding the CDR3 loop.

General significance

In addition to the general applicability of the GSS algorithm, which can bring together functional and sequence data to locate hot spots of constrained evolution, the relationship between CDR3 and scaffold discussed here should be taken into account in protein engineering when designing antibody libraries.     

Evaluating success of various restorative interventions through drone‐ and field‐collected data,using six putative framework species in Argentinian Patagonia

Field data and unmanned aerial vehicles, also known as drones, were used to analyze a long‐term experiment in a severely degraded area of the “Monte,” one of the most arid and degraded biomes in Argentina. Field methods and drone orthoimages obtained from flights of a quadcopter at 20 and 40 m were used to compare plantation plots versus natural recovery on scarified sites, and the field performance of six putative framework species under four different treatments was evaluated. After 5 years of recovery in soils with almost no organic matter and mean annual rainfall averaging 145 mm, plantation plots had high survival rates (>65%) for all species as determined through both field survey and drone imagery. Three species were planted with a greater number of seedlings due to their availability in nurseries. For these species experimental treatments were studied statistically. Independently of treatment applied (control; 1/2 L hydrogel; 1 L hydrogel; 1 L of hydrogel + 1/2 kg of organic compost), highest survival rates were found for P. flexuosa var. depressa (88% ± 14.8) and A. lampa (84% ± 14.8). Drone images and field data both showed that these two putative framework species had the highest plant cover. In sharp contrast, mechanical scarification without planting or other treatments induced very low recovery (<2%). We demonstrate that drone imagery provides a new and very valuable tool for evaluating and monitoring restorative interventions in drylands.